MNI coordinates for AAL2 scouts

[contsili]

Dear Francois,

I want to find the MNI coordinates of each AAL2 scout. My source model is dSPM.
For this reason, in Brainstorm I click my dSPM model and then press on the scout tab: Scout -> Export as MRI mask. Then I save the exported file in NIfTI format. I can open this file with spm12 or Mango (https://ric.uthscsa.edu/mango/) and view the voxel dimensions and the origin of my subject's exported MRI mask.

My questions are:

1. Do the coordinates of the exported file belong to the MNI coordinate system?
2. Is there a Brainstorm function or a script that calculates the center of mass of each AAL2 scout in MNI coordinates if I know the voxel dimensions and the origin of my subject's exported MRI mask?

Kind regards,
Konstantinos Tsilimparis

[Francois]

Do the coordinates of the exported file belong to the MNI coordinate system?

Most likely not.

Is there a Brainstorm function or a script that calculates the center of mass of each AAL2 scout in MNI coordinates

From the cortex surface, you can get:

• sSurf.Vertices: the coordinates of all the vertices of the cortex
  https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#On_the_hard_drive:_Surface
• iVertex = sSurf.Atlas(iAtlas).Scout(iScout).Vertices: The list of vertex indices corresponding to a given scout in a given atlas
• iSeed = sSurf.Atlas(iAtlas).Scout(iScout).Seed: The index of the vertex at the center of the scout, where the scout label is printed (this info is not reliable as the center of mass of the ROI)
  https://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#On_the_hard_drive

From this, you can get the SCS coordinates for all the vertices within a scout:
XYZscs = sSurf.Vertices(iVertices,:)

And then convert that to MNI coordinates (you need the MRI structure as well):
XYZmni = cs_convert(sMri, 'scs', 'mni', XYZscs);
https://neuroimage.usc.edu/brainstorm/CoordinateSystems#Converting_between_coordinate_systems